Transmission electron microscope (TEM) tomography was used to visualize the morphology and 3D connectivity of a lithographically templated, self-assembled bilayer film of cylinder-forming 45.5 kg/mol polystyrene-block polydimethylsiloxane. The structure, formed after a 5 min solvothermal anneal, was imaged with a resolution of approximate to 3 nm in 3D, enabling a comparison between measurement and self-consistent mean-field theory (SCFT) calculations. Images of etched and unetched samples showed that etching collapsed the PDMS microdomain structure and reduced the template dimensions. In addition to the general comparison between modeled and measured dimensions, the tomography revealed connections between the orthogonal layers of cylinders at their crossing points. Comparison with the SCFT model, even under solvothermal annealing conditions, shows that it is helpful in understanding the detailed nanoscale structure of features created by directed self-assembly (DSA), which is essential in developing nanomanufacturing processes based on DSA.